Double receptor polynucleotide assay method

ABSTRACT

A method for the detection of a polynucleotide target sequence is described. The method involves the formation of a covalent or non-covalent bonded pair of nucleotide sequences formed in response to a target polynucleotide sequence, adding nucleotide sequence specific binding proteins each capable of binding one member of the pair of nucleotide sequences, and detecting the specific binding proteins complexed to the pair of nucleotide sequences.

This is a divisional of pending application Ser. No. 08/051,512, filedApr. 22, 1993, which in turn is a continuation of abandoned applicationSer. No. 07/511,651, filed Apr. 20, 1990.

FIELD OF THE INVENTION

This invention relates to methods for determining the presence ofpolynucleotides such as a target polynucleotide sequence in a sample andcompositions and kits relating thereto.

BACKGROUND OF THE INVENTION

Methods have been described for causing two nucleic acid strands tobecome associated as a result of the presence of a targetpolynucleotide. These methods are based on forming a noncovalentsandwich involving the target and two probes, each binding to adifferent site on the target. If the probes are contiguous or separatedby one nucleotide, they can be joined in a covalent sandwich by a ligase(Goffin, C. et.al. Nucleic Acids Res. 15(21): 8755 (1987)). The ligatedprobe can then be amplified using known technology (Saiki, et al.,Science 230:1350 (1986)). Regardless of whether the probes are ligatedor amplified, provided they are covalently or non-covalently bound, theclose association of the two probes can be detected by such knownmethods as enzyme channeling, fluorescence energy transfer and the like.

Various hybridization methods have been used in order to detect nucleicacid sequences. European Patent Application 0,192,168 describes asolution phase dual hybridization assay for the detection ofpolynucleotide sequences. The method described uses a separation probewhich carries a reactive site capable of forming a stable covalent ornon-covalent bond with a reaction partner. In the preferred practice ofthe invention, the reaction partner is attached to a solid support bycovalent or non-covalent bonds.

World Patent Application 87/03622 describes a hybridization assay whichresults in high levels of amplification. Amplification is achieved bytaking a primary probe, a small segment of which is hybridized to thetarget DNA of interest and introducing a second probe which recognizes aseparate segment of the target. Using the dual probe system, increasedamplification occurs upon the hybridization event taking place.

U.S. Pat. No. 4,775,619 describes a method for the detection of aspecific sequence using a hybridization technique such that duplexing ofthe sample DNA and a probe affects the ability to modify the spatialrelationship between a label and a support. The presence of the specificsequence, the target polynucleotide, is determined by the amount oflabel released into the medium.

U.S. Pat. No. 4,766,062 describes a method for determining the presenceof a target polynucleotide in a sample wherein the probe polynucleotidecomplex is capable of base pair binding such that the targetpolynucleotide binds to the probe with a displacement of the labeledpolynucleotide from the complex. In order for the detection system to besuccessful there must be sufficient base-pair binding to the targetsystem in order to generate the release of a detectable signal.

Yet another method for the detection of nucleic acid hybridization isdescribed in U.S. Pat. No. 4,724,202. The patent describes a method ofdetection in which the known sample or separation probe is immobilizedon a solid support and contacted with a mixture containing the unknownand a labeled detection probe. The labeled detection probe is createdwithout the use of radioactivity and without chemical modfication byhaving a single-stranded portion of nucleic acid capable of hybridizingwith the unknown connected with a non-hybridizable single or doublestranded nucleic acid portion. The non-hybridizable portion includes arecognition site for a particular protein.

A method for detecting the presence of a target nucleotide sequence in apolynucleotide which comprises hybridizing a first nucleotide sequenceand a second nucleotide sequence to non-contiguous portions of a targetnucleotide sequence and detecting the presence of such first and secondnucleotide sequences is set forth in U.S. patent application Ser. No.07/236,967 now U.S. Pat. No. 5,185,243, the disclosure of which isincorporated herein by reference.

None of the cited background art, however, provide a solution to theproblem of detection of nucleic acids as described by the presentinvention. Using the methods of the present invention, a targetpolynucleotide sequence can be detected using the solution phasehybridization protocol which may be easily adapted to large scaleimmunochemical analysis. The methods described in the present inventioncan be easily applied to the design of diagnostic test systems.

SUMMARY OF THE INVENTION

One embodiment of the invention is a method for detecting a targetpolynucleotide sequence which method comprises: (a) forming in responseto a target polynucleotide sequence a covalently or noncovalently bondedpair of nucleotide sequences for a portion of each of which exist anucleotide sequence specific binding protein (NSSBP); and (b) detectingthe NSSBPs complexed to the bonded pair of nucleotide sequences.

Another embodiment of the invention describes a method for detecting atarget polynucleotide sequence in a medium suspected of containing thetarget polynucleotide sequence. The method comprises: (a) hybridizing tothe 3' end of the target polynucleotide sequence a first ligand bound tothe 3' end of a first specific nucleotide sequence wherein the specificnucleotide sequence is single stranded; (b) extending the targetpolynucleotide sequence by means of a template dependent polynucleotidepolymerase and nucleoside triphosphates along the single stranded firstspecific nucleotide sequence thereby forming a double stranded firstspecific nucleotide sequence; (c) combining with the double strandedfirst specific nucleotide sequence, if not already combined, a secondligand bound to a second specific nucleotide sequence, and NSSBPscapable of binding the double stranded first and second specificnucleotide sequences; and (d) detecting the complex of the NSSBPs with abound pair of double stranded first and second specific nucleotidesequences.

In another embodiment of the invention a method for detecting a targetpolynucleotide sequence in a sample is described which comprises: (a)providing in combination in a liquid medium a first ligand having asequence hybridizable with a first portion of the target polynucleotidesequence and bound to a first specific nucleotide sequence, and a secondligand having a sequence hybridizable with a second portion of thetarget sequence and bound to a second specific nucleotide sequence; (b)providing means for linking the first and second ligands as a functionof the presence of the target sequence; (c) combining with the linkedfirst and second ligands, first and second NSSBPs capable of bindingrespectively to the first and second specific binding sequences; and (d)detecting binding between the linked NSSBPs, the detection thereofindicating the presence of the target polynucleotide sequence in thesample.

In another embodiment of the invention is described a method fordetecting a bonded pair of polynucleotide sequences comprising thedetection of binding of NSSBPs to two specific nucleotide sequences thatcomprise separate portions of the bonded pair of polynucleotidesequences.

In still another embodiment of the invention a method for performing anassay for a bonded pair of polynucleotide sequences comprised of firstand second specific nucleotide sequences in a sample suspected ofcontaining the bonded pair is described. The method comprises: (a)combining in a liquid medium (1) the sample, (2) first and second NSSBPscapable of binding, respectively, to the first and second specificnucleotide sequences wherein the first NSSBP is bound or capable ofbinding to a surface and the second NSSBP is bound to or capable ofbinding to a detectable label, and (3) the surface; (b) separating themedium from the surface; (c) combining the surface with a detectablelabel capable of binding the second NSSBP, when the second NSSBP is notalready bound to a label; and (d) detecting the label bound to thesurface.

Another embodiment of the invention describes a composition comprising atarget polynucleotide bound to specific nucleotide sequences each boundto its respective NSSBP wherein one of the NSSBPs is bound to or iscapable of binding to a surface and the other NSSBP is bound to or iscapable of binding to a label.

In another embodiment of the invention is described a kit for use indetermining a target nucleotide sequence which comprises in packagedcombination (1) a pair of nucleotide sequences for a portion of each ofwhich exists a different NSSBP, and (2) the different nucleotidespecific binding proteins.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: Detection of a target polynucleotide sequence by hybridizationof the target polynucleotide sequence with a pre-formed double stranded1st and 2nd specific nucleotide sequence.

FIG. 2: Detection of a target polynucleotide sequence by covalentattachment, either chemical or enzymatic, of a 1st and 2nd specificnucleotide sequence to the target polynucleotide sequence.

FIG. 3: Detection of a target nucleotide sequence by extension down oneside of a 1st specific polynucleotide sequence.

FIG. 4: Schematic of embodiment of the invention as more fully describedin Example 1.

FIG. 5: Schematic of embodiment of the invention as more fully describedin Example 2.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

As set forth below, and for convenience in describing this invention,the following terms are defined as follows:

"Target polynucleotide sequences" shall mean all or a portion of asequence of nucleotides to be identified, the identity of which is knownto a sufficient extent so as to allow the preparation of a bindingpolynucleotide sequence that is complementary to and will hybridize withsuch target polynucleotide sequence. The target polynucleotide sequenceusually will contain from about 12 to 1000 or more nucleotides,preferably 15 to 50 nucleotides. The target polynucleotide sequence mayor may not be a portion of a larger molecule.

"Bonded pair of polynucleotide sequences" shall mean a first and asecond polynucleotide sequence which become bonded together as a resultof the presence of the target polynucleotide sequence. The bonding ofthe first and second polynucleotide sequences to form the bonded paircan be covalent or non-covalent.

"First ligand" shall mean a portion of a first polynucleotide sequencethat is capable of hybridizing with the target nucleotide sequence byvirtue of having a polynucleotide sequence complementary to a region ofthe target nucleotide sequence such that the first ligand will becomebound to such region of the target nucleotide.

"Second ligand" shall mean a portion of a second polynucleotide sequencethat is capable of hybridizing with the target nucleotide sequence at aregion other than that of the first ligand.

"Ligation" shall mean the covalent attachment between the first andsecond nucleotide sequence. The chemical bonds are formed when thesequences are bound to the target polynucleotide sequence. Covalentattachment can be achieved enzymatically, as in a ligation catalyzed byT4 DNA ligase or E. coli DNA ligase in the presence of the necessarycofactors, or chemically.

One means for chemically forming the covalent attachment between thefirst and second nucleotide sequences is by use of a photoreaction. Forexample, one of the contiguous nucleotides can be treated to form anaryl azide and then the material can be irradiated to result in acovalent bond formation between the contiguous nucleotides.

Another means for achieving the covalent attachment of the first andsecond nucleotide sequences when the sequences are hybridized tonon-contiguous portions of the target nucleotide sequence involves theuse of a nucleotide sequence that is sufficiently complementary to thenon-contiguous portion of the target nucleotide sequence lying betweenthe first and second nucleotide sequences. For purposes of thisdescription such a nucleotide sequence will be referred to as anintervening linker sequence. The linker sequence can be hybridized tothe target sequence between the first and second nucleotide sequences.The linker sequence can then be covalently attached to both the firstand second nucleotide sequence utilizing enzymatic or chemical means asreferred to above. It is also possible to utilize combinations of linkersequences and polymerase to achieve a contiguous relationship betweenthe first and second nucleotide sequences when these sequences are boundto the target nucleotide sequence.

Another means for covalently attaching the first and second nucleotidesequences when the sequences are hybridized to the target nucleotidesequence in a non-contiguous relationship involves chain extension ofthe second nucleotide sequence followed by carbodiimide coupling of thetwo sequences as described by Dolinnaya, et al. (1988), Nucleic AcidsResearch, 16 (9): 3721-3938.

"Specific nucleotide sequences" shall mean portions of the first andsecond polynucleotide sequences that are bonded to and may include aportion of the first and second ligands and are capable of binding tonucleotide sequence specific binding proteins, or can become capable ofbinding to nucleotide sequence specific binding proteins when hybridizedto a complementary polynucleotide sequence.

"Nucleotide sequence specific binding proteins (NSSBP)" shall meanproteins which recognize and are capable of binding specifically to thespecific nucleotide sequences. Preferred pairs of NSSBPs and specificnucleotide sequences are, for example, repressors and operators, such asthe tetracycline (tet) repressor, β-galactosidase (lac repressor), andthe tryptophan (trp) repressor and their corresponding double-strandedDNA operator sequences. In addition, the lambda specific repressorprotein, CRO, and the catabolite activator protein, CAP, may be used.

"Operators" shall mean specific nucleotide sequences that bind repressorproteins. Operators are generally found adjacent to structural genescoding for enzymes and other proteins employed in cell metabolism andcell structure. The structural and regulatory genes that are involved ina particular cell function and are clustered together on the genetic mapconstitute a coordinate set of genes designated an operon. Control overtranscription is dependent upon repressor proteins that interact withthe operator immediately adjacent the genes coding for enzymes and otherproteins needed for metabolism.

"Repressors" shall mean proteins which interact and bind to theoperators. A repressor is specific for its own operator, and differentoperators are bound by different repressors. Examples ofoperator-repressor systems include lac, trp, CRO, tet and the like.

"Signal Producing System" shall consist of one or more components, atleast one component being a label or reporter group. The signalproducing system generates a signal that relates to the presence oramount of target polynucleotide in a sample. The signal producing systemincludes all of the reagents required to produce a measurable signal.The operation of the signal producing system is to produce a detectablesignal related to the presence or amount of target polynucleotide in thesample.

"Non-contiguous binding" shall describe the binding wherein the firstand second ligand are hybridized to the target polynucleotide sequencein a manner whereby the 3' terminal base of either the first or secondligand and the 5' terminal base of the other of said ligands are nothybridized to adjacent bases of the target polynucleotide sequence.

"Nucleoside triphosphates" shall describe a nucleoside having a 5'triphosphate substituent, usually a deoxynucleoside triphosphate. Thenucleosides are pentose sugar derivatives of nitrogenous bases of eitherpurine or pyrimidine derivation, covalently bonded to the 1'-carbon ofthe pentose sugar. The purine bases include adenine(A), guanine(G), andderivatives and analogs thereof. The pyrimidine bases include cytosine(C), thymine (T), uracil (U), and derivatives and analogs thereof.

"Template-dependent polynucleotide polymerase" shall mean a catalyst,usually an enzyme, for forming an extension of the primarypolynucleotide sequence or the target polynucleotide sequence, as thecase may be, along the single stranded pattern polynucleotide where theextension is complementary to the template sequence. Thetemplate-dependent polynucleotide polymerase utilizes the nucleosidetriphosphates as the building blocks for the extension which proceeds ina 5' to 3' (3' to 5' with respect to the template) direction untilextension terminates. Usually, the catalysts are enzymes, such as RNApolymerases, preferably DNA polymerases such as, for example,prokaryotic DNA polymerase (I, II, or III), T4 DNA polymerase, T7 DNApolymerase, Klenow fragment, reverse transcriptase, RNA replicases, andthe like derived from any source such as cells, bacteria, such as E.coli, plants, animals, virus, thermophilic bacteria, and so forth.

Particular Embodiments

One embodiment of the present invention regards a general method fordetermining if two probe polynucleotide sequences have become linked asa function of the presence of a target polynucleotide sequence. In sucha method, a portion of a first polynucleotide sequence is a ligand for atarget polynucleotide sequence and a portion of a second polynucleotidesequence is a different ligand for a different portion of the targetpolynucleotide sequence. Additionally, the first and secondpolynucleotide sequences each have different specific nucleotidesequences. Usually the ligand sequences will be single stranded. Thefirst and second polynucleotide sequences form a bonded pair ofpolynucleotide sequences upon binding to different portions of the sametarget polynucleotide sequence. The bonding can be covalent ornon-covalent. Covalent bonding can be achieved by causing the twopolynucleotide sequences to both bind to the target polynucleotidesequence with subsequent target dependent ligation of the polynucleotidesequences to one another. An example of a bonded pair of polynucleotidesequences produced in this embodiment is illustrated in FIG. 1, whereinA is a target polynucleotide sequence, B is a first (1st) ligand, C is asecond (2nd) ligand, D is a first (1st) specific nucleotide sequence, Eis a second (2nd) specific nucleotide sequence and D and E represent abonded pair of polynucleotide sequences, and FIG. 2, wherein A is atarget polynucleotide sequence, B is a first (1st) ligand, C is a second(2nd) ligand, D is a first (1st) specific nucleotide sequence, E is asecond (2nd) specific nucleotide sequence and D and E represent a bondedpair of polynucleotide sequences, and F is a covalent bond or bridge.Non-covalent bonding is achieved through base pairing.

Preferred pairs of NSSBPs and specific nucleotide sequences arerepressors and operators, such as the tetracycline (tet) repressor,β-galactosidase (lac repressor), and the tryptophan (trp) repressor andtheir corresponding double-stranded DNA operator sequences. In addition,the lambda specific repressor protein, CRO, and the catabolite activatorprotein, CAP, may be used. Alternatively, restriction enzymes and thecorresponding restriction sites can be used under conditions where thenuclease activity of the enzyme is suppressed.

In one aspect of the invention, one NSSBP is bound to a surface and theother NSSBP is bound to a label selected to provide a detectable eventwhen a bonded pair of polynucleotide sequences is present. For example,each NSSBP can be on the surface of a separate set of particles whereco-aggregation of the two sets provides a detectible signal that differsfrom self-aggregation or no aggregration of the sets of particles.

In another aspect of the invention, the bonded pair of polynucleotidesequences can be detected by pairs of interactive labels, one bound toeach NSSBP, such as, for example, a fluorescer or chemiluminescer and anenergy acceptor; two enzymes capable of channeling, i.e., the product ofone acts as the substrate of the other; an enzyme and a polycation orpolyanion capable of changing the microscopic pH and affecting enzymeactivity; a particle and a polycation or anion capable of causingparticle agglutination, and the like. Binding of the labels to the NSSBPmay be covalent or noncovalent and where noncovalent, may involveligand-receptor binding pairs, such as antibody-antigen, biotin-avidin,DNA hybridization, and the like.

In another application of the present invention (FIG. 3), binding of aNSSBP to a specific nucleotide sequence can occur only when the sequenceis double stranded. In FIG. 3, A is a target polynucleotide sequence, Bis a first (1st) specific nucleotide sequence, C is a second (2nd)specific nucleotide sequence, D is a second (2nd) ligand, TDPNP istemplate-dependent polynucleotide polymerase, d×TPs are nucleosidetriphosphates and ** represents blocked so as to disallow extension. Thefirst and second polynucleotide sequences are capable of binding thetarget polynucleotide sequence. The first polynucleotide sequence issingle stranded and is composed of a first ligand that is bound to the3' end of the first specific nucleotide sequence and is capable ofhybridizing with the 3' end of the target polynucleotide sequence. Aftercausing at least the first polynucleotide sequence to hybridize with thetarget sequence, polynucleotide dependent nucleotide polymerase andnucleoside triphosphates are added to cause chain extension of thetarget sequence along the first polynucleotide sequence to form a doublestranded specific nucleotide sequence. The second polynucleotidesequence is then caused to hybridize with the target sequence, if notcarried out previously, thereby forming a bonded pair of polynucleotidesequences. NSSBPs capable of specifically binding the specificnucleotide sequences in the bonded pair are then added and detection ofsimultaneous binding to the bonded pair is carried out as describedabove.

Generally, a combination is provided in a liquid medium comprising asample suspected of containing a target polynucleotide sequence, a firstpolynucleotide sequence complementary to a first portion of the targetpolynucleotide sequence, a second polynucleotide sequence complementaryto a portion of the target polynucleotide sequence other than the firstportion and means for hybridizing the first and second sequences withthe target polynucleotide sequence.

The order of combining of the various reagents to form the combinationmay vary and can be simultaneous or wholly or partially sequential.Generally, a sample containing a target polynucleotide sequence isobtained. This may be combined with a pre-prepared combination of firstand second nucleotide sequences, nucleoside triphosphates, andpolynucleotide polymerase. Following these additions a ligase or othermeans to produce ligation can optionally be employed. Simultaneousaddition of the above, as well as other step-wise or sequential ordersof addition, may be employed. The concentration and order of addition ofreagents and conditions for the method are governed generally by thedesire to optimize hybridization of all the first and second nucleotidesequences with the target nucleotide sequence.

In carrying out the method of the invention an aqueous medium will beemployed. The pH for the medium will usually be in the range of about4.5 to 9.5, more usually in the range of about 5.5-8.5, and preferablyin the range of about 6-8. The pH and temperature are chosen and varied,as the case may be, so as to provide for either simultaneous orsequential hybridization of the target sequence with the first andsecond polynucleotide sequences or extension of the first and secondpolynucleotide sequence along the target polynucleotide sequence.Various buffers may be used to achieve the desired pH and maintain thepH during the determination. Illustrative buffers include borate,phosphate, carbonate, Tris, barbital and the like. The particular bufferemployed is not critical to this invention but in individual methods onebuffer may be preferred over another.

Moderate temperatures are normally employed for carrying out the methodand desirably constant temperatures during the period for conducting themethod. The temperatures for the method will generally range from about20° to 90° C., more usually from about 30° to 70° C. preferably 37° to50° C. However, the temperature can be varied depending on whether theabove steps are carried out sequentially or simultaneously. For example,relatively low temperatures of from about 20° to 40° C. can be employedfor the chain extension step, while denaturation and hybridization canbe carried out at a temperature of from about 40° to 80° C.

The time period for carrying out the method of the invention willgenerally be long enough to achieve attachment between the first andsecond polynucleotide sequences, when these sequences are attached tothe target polynucleotide sequence and determining whether suchattachment has occurred. Generally, the time period for conducting themethod will be from about 5 to 200 min. As a matter of convenience, itwill usually be desirable to minimize the time period.

The concentration of the target polynucleotide sequence to be determinedcan be as low as 10⁻²¹ M in a sample but will generally vary from about10⁻¹⁴ M to 10⁻¹⁹ M, more usually from about 10⁻¹⁶ to 10⁻¹⁹ M. Theconcentration of the first and second polynucleotide sequence and thedeoxynucleoside triphosphates in the medium can vary widely. Preferably,these reagents will be present in large molar excess over the amount oftarget polynucleotide sequence expected. The deoxynucleosidetriphosphates will usually be present in 10⁻⁶ to 10⁻² M, preferably 10⁻⁵to 10⁻³ M. The second polynucleotide sequences, as well as the firstpolynucleotide sequence, will usually be present in at least 10⁻¹² M,preferably 10⁻¹⁰ M, more preferably at least about 10⁻⁸ M.

The concentration of the polymerase and any cofactors in the medium canalso vary substantially. These reagents may be present in as low as10⁻¹² M but may be present in a concentration at least as high or higherthan the concentration of the first and second polynucleotide sequences,the primary limiting factor being the cost of the reagents, which areusually enzymes. The final concentration of each of the reagents willnormally be determined empirically to optimize the present method withrespect to both speed and sensitivity.

When used together with target mediated ligation and single primeramplification, the methods of the present invention provide ahomogeneous DNA assay procedure. In general, the assay procedureconsists of mixing together sample containing the target nucleotidesequence under conditions which cause complexation of the probes withthe target. A ligase is added to cause linking of probes to boundtarget. Nucleoside triphosphates are added together with a primercontaining the complementary sequence at its 3' end and a nucleotidepolymerase. Conditions are provided to cause amplification of theligated sequence, which comprises the first ligand and second ligandbonded at their 5' and 3' ends, respectively. (See, for example, U.S.Ser. No. 07/236,967 incorporated herein by reference.)

In one application of the present invention, protein receptors capableof binding to the first ligand and the second ligand, usually whencomplexed with a complementary sequence, are combined where the firstand second ligands are labeled according to any of the above methodsthat allow homogeneous detection, e.g., fluorescent beads and carbonparticles, enzymes that can channel, and the like.

The signal associated with binding to the first and second specificnucleotide sequence is detected without separation from the assaymedium. Detection of the signal will depend upon the nature of thesignal producing system utilized. If the label or reporter group is anenzyme, additional members of the signal producing system would includeenzyme substrates and so forth. The product of the enzyme reaction ispreferably a dye that can be detected spectrophotometrically. If thelabel is a fluorescent molecule the medium can be irradiated and thefluorescence determined. Where the label is a radioactive group, themedium can be counted to determine the radioactive count.

The reagents employed in the present invention can be provided in a kitin packaged combination with predetermined amounts of reagents for usein the present method in assaying for a target polynucleotide sequencepresent in a sample. For example, a kit useful in the present method cancomprise in packaged combination with other reagents, first and secondpolynucleotide sequences and the corresponding nucleotide sequencespecific binding proteins. The kit can further include in the packagedcombination nucleoside triphosphates such as deoxynucleosidetriphosphates, e.g., deoxyadenosine triphosphate (dATP), deoxyguanosinetriphosphate (dGTP), deoxycytidine triphosphate (dCTP) anddeoxythymidine triphosphate (dTTP). The kit can further include apolynucleotide polymerase and also means for covalently attaching thefirst and second sequences, such as a ligase.

The relative amounts of the various reagents in the kits can be variedwidely to provide for concentrations of the reagents which substantiallyoptimize the reactions that need to occur during the present method andto further substantially optimize the sensitivity of the assay. Underappropriate circumstances one or more of the reagents in the kit can beprovided as a dry powder, usually lyophilized, including excipients,which on dissolution will provide for a reagent solution having theappropriate concentrations for performing a method or assay inaccordance with the present invention. Each reagent can be packaged inseparate containers or some reagents can be combined in one containerwhere reactivity and shelf life will permit.

The assay described in the present invention can be used to detectspecific target polynucleotide sequences comprising a portion of thesample of interest. The sample of interest may be used directly wherethe target polynucleotide is single stranded or may be treated todenature double stranded target sequences and optionally cleave thetarget to obtain a fragment that contains a target polynucleotidesequence. The sample can be cleaved by known techniques such astreatment with a restriction endonuclease or other site specificchemical or enzymatic cleavage methods.

The target polynucleotide sequence may comprise a portion of, forexample, nucleic acids from any source in purified or unpurified formincluding DNA (dsDNA and ssDNA) and RNA, including t-RNA, m-RNA, r-RNA,mitochondrial DNA and RNA, chloroplast DNA and RNA, DNA-RNA hybrids, ormixtures thereof, genes, chromosomes, plasmids, the genomes ofbiological material such as microorganisms, e.g., bacteria, yeasts,viruses, viroids, molds, fungi, plants, animals, humans, and fragmentsthereof, and the like. The target polynucleotide sequence can be only aminor fraction of a complex mixture such as a biological sample. Thetarget polynucleotide sequence can be obtained from various biologicalmaterial by procedures well known in the art. Some examples of suchbiological material by way of illustration and not limitation aredisclosed in Table I below.

    __________________________________________________________________________    Microorganisms of interest include:                                           __________________________________________________________________________    Corynebacteria                                                                Corynebacterium diphtheria                                                    Pneumococci                                                                   Diplococcus pneumoniae                                                        Streptococci                                                                  Streptococcus pyrogenes                                                       Streptococcus salivarus                                                       Staphylococci                                                                 Staphylococcus aureus                                                         Staphylococcus albus                                                          Neisseria                                                                     Neisseria meningitidis                                                        Neisseria gonorrhea                                                           Enterobacteriaciae                                                            Escherichia coli                                                              Aerobacter aerogenes                                                                              The colliform                                             Klebsiella pneumoniae                                                                             bacteria                                                  Salmonella typhosa                                                            Salmonella choleraesuis                                                                           The Salmonellae                                           Salmonella typhimurium                                                        Shigella dysenteria The Shigellae                                             Shigella schmitzii                                                            Shigella arabinotarda                                                         Shigella flexneri                                                             Shigella boydii                                                               Shigella sonnei                                                               Other enteric bacilli                                                         Proteus vulgaris    Proteus species                                           Proteus mirabilis                                                             Proteus morgani                                                               Pseudomonas aeruginosa                                                        Alcaligenes faecalis                                                          Vibrio cholerae                                                               Hemophilus-Bordetella group                                                                       Rhizopus oryzae                                           Hemophilus influenza, H. ducryi                                                                   Rhizopus arrhizua Phycomycetes                            Hemophilus hemophilus                                                                             Rhizopus nigricans                                        Hemophilus aegypticus                                                                             Sporotrichum schenkii                                     Hemophilus parainfluenza                                                                          Flonsecaea pedrosoi                                       Bordetella pertussis                                                                              Fonsecacea compact                                        Pasteurellae        Fonsecacea dermatidis                                     Pasturella pestis   Cladosporium carrionii                                    Pasteurella tulareusis                                                                            Phialophora verrucosa                                     Brucellae           Aspergillus nidulans                                      Brucella melitensis Madurella mycetomi                                        Brucella abortus    Madurella grisea                                          Brucella suis       Allescheria boydii                                        Aerobic Spore-forming Bacilli                                                                     Phialophora jeanselmei                                    Bacillus anthracis  Microsporum gypseum                                       Bacillus subtilis   Trichophyton mentagrophytes                               Bacillus megaterium Keratinomyces ajelloi                                     Bacillus cereus     Microsporum canis                                         Anaerobic Spore-forming Bacilli                                                                   Trichophyton rubrum                                       Clostridium botulinum                                                                             Microsporum adouini                                       Clostridium tetani  Viruses                                                   Clostridium perfringens                                                                           Adenoviruses                                              Clostridium novyi   Herpes Viruses                                            Clostridium septicum                                                                              Herpes simplex                                            Clostridium histolyticum                                                                          Varicella (Chicken pox)                                   Clostridium tertium Herpes Zoster (Shingles)                                  Clostridium bifermentans                                                                          Virus B                                                   Clostridium sporogenes                                                                            Cytomegalovirus                                           Mycobacteria        Pox Viruses                                               Mycobacterium tuberculosis                                                                        Variola (smallpox)                                        hominis                                                                       Mycobacterium bovis Vaccinia                                                  Mycobacterium avium Poxvirus bovis                                            Mycobacterium leprae                                                                              Paravaccinia                                              Mycobacterium paratuberculosis                                                                    Molluscum contagiosum                                     Actinomycetes (fungus-like bacteria)                                                              Picornaviruses                                            Actinomyces Isaeli  Poliovirus                                                Actinomyces bovis   Coxsackievirus                                            Actinomyces naeslundii                                                                            Echoviruses                                               Nocardia asteroides Rhinoviruses                                              Nocardia brasiliensis                                                                             Myxoviruses                                               The Spirochetes     Influenza (A, B, and C)                                   Treponema pallidum Spirillum minus                                                                Parainfluenza (1-4)                                       Treponema pertenue Streptobacillus                                                                Mumps Virus                                               monoiliformis       Newcastle Disease Virus                                   Treponema carateum  Measles Virus                                             Borrelia recurrentis                                                                              Rinderpest Virus                                          Leptospira icterohemorrhagiae                                                                     Canine Distemper Virus                                    Leptospira canicola Respiratory Syncytial Virus                               Trypanasomes        Rubella Virus                                             Mycoplasmas         Arboviruses                                               Mycoplasma pneumoniae                                                         Other pathogens                                                               Eastern Equine Eucephalitis Virus                                             Listeria monocytogenes                                                        Western Equine Eucephalitis Virus                                             Erysipelothrix rhusiopathiae                                                  Sindbis Virus                                                                 Streptobacillus moniliformis                                                  Chikugunya Virus                                                              Donvania granulomatis                                                         Semliki Forest Virus                                                          Bartonella bacilliformis                                                      Mayora Virus                                                                  Rickettsiae (bacteria-like                                                    St. Louis Encephalitis Virus                                                  parasites)                                                                    Rickettsia prowazekii                                                         California Encephalitis Virus                                                 Rickettsia mooseri                                                            Colorado Tick Fever Virus                                                     Rickettsia rickettsii                                                         Yellow Fever Virus                                                            Rickettsia conori                                                             Dengue Virus                                                                  Rickettsia australis                                                          Reoviruses                                                                    Rickettsia sibiricus                                                          Reovirus Types 1-3                                                            Retroviruses                                                                  Rickettsia akari                                                              Human Immunodeficiency Viruses (HIV)                                          Rickettsia tsutsugamushi                                                      Human T-cell Lymphotrophic                                                    Virus I & II (HTLV)                                                           Rickettsia burnetti                                                           Hepatitis                                                                     Rickettsia quintana                                                           Hepatitis A Virus                                                             Chlamydia (unclassifiable parasites                                                               Hepatitis B Virus                                         bacterial/viral)                                                              Hepatitis nonA-nonB Virus                                                     Chlamydia agents (naming uncertain)                                                               Tumor Viruses                                             Fungi                                                                         Rauscher Leukemia Virus                                                       Cryptococcus neoformans                                                       Gross Virus                                                                   Blastomyces dermatidis                                                        Maloney Leukemia Virus                                                        Hisoplasma capsulatum                                                         Coccidioides immitis                                                          Human Papilloma Virus                                                         Paracoccidioides brasiliensis                                                 Candida albicans                                                              Aspergillus fumigatus                                                         Mucor corymbifer (Absidia corymbifera)                                        __________________________________________________________________________

The double receptor polynucleotide assay method as described byinvention provides a simple and straight forward assay method easilyadaptable to a diagnostic testing system. The specific target nucleotidesequence identified using this assay method will frequently becharacteristic of a particular disease state, genetic characteristic orabnormality.

EXAMPLES

The following examples are illustrative, and not limiting of theinvention. General conditions for nucleic acid hybridization and the useof DNA and RNA modifying enzymes can be found in Molecular Cloning: ALaboratory Manual by Sambrook, Fritsch and Maniatis, 2nd Edition, ColdSpring Harbor Laboratory Press (1989).

Unless otherwise described, the following materials and methods forproduction of necessary reagents of use in carrying out the inventionare known in the art and can be obtained as follows:

The lactose repressor protein may be prepared as described in theliterature:

Rosenberg, J. M. et al. Nucleic Acid Res. 4(3):567 (1977)

Matthews, K. S., J. Biol. Chem. 253(12):4279 (1978)

O'Gorman, R. B. et al. J. Biol. Chem. 255(21):10100 (1980)

Levens, D. and P. M. Howley, Mol. Cell. Biol. 5(9):2307 (1985)

The presence, activity and degree of purity of the lactose repressorprotein prepared using the above referenced methods can be determinedusing procedures described in the literature. In particular, Bourgeois,S. and A. D. Riggs, Biochem. Biophys. Res. Comm. 38(2):348 (1970);Barkley, M. D. and S. Bourgeois in The Operon, Cold Spring Harbor, N.Y.pp. 177-220 (1978); and Bourgeois, S. in Methods in Enzymology Vol. 21,pp. 491-500 (1971).

The tetracycline (tet) repressor protein may be prepared as described inthe literature:

Hillen, W., et al. J. Mol. Biol. 257(11):6605 (1982)

Oehmichen, R. et al. EMBO J. 3(3):539 (1984)

The tet repressor protein may be assayed and characterized as describedby:

Altschemied, L. and W. Hillen, J. Mol. Biol. 187:341 (1986)

Hillen, W. et al. J. Mol. Biol. 172:185 (1984)

Hillen, W. et al. J. Mol. Biol. 169:707 (1983)

EXAMPLE 1

The presence or absence of the target DNA in a sample is determined byadding an aliquot of sample to a convenient volume of hybridizationbuffer, for example, 10 mM Tris (pH 7.5), 1 mM EDTA. The hybridizationbuffer will also contain approximately 1 mM of the first and secondligand containing nucleic acid sequences such as are shown in FIGS. 1and 2. In one application of the example the nucleotide sequence of theD and E regions (see FIGS. 1 and 2) are those of lactose (lac) operatorand tetracycline (tet) operator respectively as known from and describedin the literature cited above. After denaturing any target DNA presentinto single strands by heating to approximately 98° C. for at least 2minutes, the temperature of the solution is reduced so as to allowhybridization of the ligand sequence to any target nucleic acid presentin the sample. The exact hybridization temperature may be calculatedfrom the cited references considering the length of the ligand sequencesto be hybridized to the target and the % AT base composition. Thereaction time necessary for substantially complete hybridization willalso typically be calculated from equations well known in the literatureand again depending on the length of the ligand sequence and itscomplexity (see, for example, Albretsen, C. et al. Anal. Blochem.170:193 (1988), Matthews, J. A. and Kricka, L. J. Anal. Biochem. 169:1(1988), Meinkoth, J. and Wahl, G. Anal. Biochem 138:267 (1984), andMiyada, C. G. and Wallace, R. B. Methods in Enzymology, 154:94 (1987)).

Following the formation of the ternary complex (as is shown in FIGS. 1and 2), the solution is cooled to room temperature and abeta-galactosidase-lac repressor fusion protein (Promega Corp., Madison,Wis.), and anti-beta-galactosidase mouse monoclonal antibody (PromegaCorp., Madison, Wis.), and a solid surface (such as a bead) immobilizedrabbit-anti-mouse antibody (RAM bead, Bio-Rad Laboratories, RichmondCalif.) are added to the mixture. The concentration of these componentsand incubation time (approximately 15 minutes) will be such that all thelac operator containing nucleic acid sequence is bound onto the solidsurface. The solid surface is separated from the liquid phase bycentrifugation. After a washing step (an equal volume of 10 mM Tris,pH=7.5, 100 mM NAGl) and centrifugation, labeled tet repressor proteinis added the tet repressor binding conditions described in theliterature and referenced above. Following incubation (typically 15minutes), removal of the unbound protein, and washing, the amount oflabeled repressor material remaining above that observed with thenegative control (i.e. lacking any sample or target nucleic acid) is ameasure of the presence and amount of target nucleic acid present in thesample.

The second repressor in this example may be labeled by modification witha fluorescent dye, a radioactive marker (such as 125-Iodine), or bymeans of a covalently attached enzyme label turning over a detectableproduct when provided with its appropriate substrates in the final stepof the detection reaction. The final cofiguration of this assay is shownwith a model duplex DNA in FIG. 4, wherein A is rabbit anti-mouseantibody, B is anti β-galactosidase antibody, C is β-galactosidase-lacrepressor fusion protein, D is target nucleotide sequence, tet is Tetrepressor protein dimer and tet_(R) Tet operator DNA sequence.

EXAMPLE 2

An alternative method of carrying out the present invention isschematically set forth in FIG. 5, wherein I.-IV. are alternate methodsof binding tet repressor protein to microtiter wells, O is tet repressorprotein dimer, O is covalently attached tet repressor protein, O-B istet repressor protein bound to biotin, A is avidin, OH is tet repressorprotein bound to hapten and =< is immobilized antibody to hapten. Inthis example, the tetracycline repressor protein is immobilized on asolid surface. This may be accomplished by passive adsorption or by theuse of a covalent bond. For examples of methods for the immobilizationof proteins see Affinity Chromatography: a Practical Approach, Dean, P.D. G. et al. eds., IRL Press, (1985), in particular, chapter 5 and thereferences contained therein.

In the example outlined in FIG. 5, the ternary complex produces as inExample 1 is added to the immobilized binding protein. After a suitableincubation time to allow binding (typically 15 minutes) and a washingstep to remove unbound material, a second DNA binding protein, forexample, the beta-galactosidate-lac repressor fusion protein is added.The second DNA binding protein is allowed to bind and washed so as toremove unbound and non-specifically bound beta-galactosidase activity. Asubstrate for beta-galactosidase is then added (for example "Bluo-gal",pNPG, or X-gal; BRL, Gaithersburg, Md.), and the presence of the targetnucleic acid is inferred from the formation of colored dye.

The above description and examples fully disclose the inventionincluding preferred embodiments thereof. Modifications of the methodsdescribed that are obvious to those of ordinary skill in molecularbiology and related sciences are intended to be within the scope of thefollowing claims.

What is claimed is:
 1. A method for detecting a bonded pair ofpolynucleotide sequences hybridized to the same target polynucleotidesequence, said method comprising the detection of simultaneous bindingof nucleotide sequence specific binding proteins (NSSBP) to two specificnucleotide sequences that comprise separate portions of the bonded pairof polynucleotide sequences hybridized to the same target polynucleotidesequence, wherein one of the NSSBPs is bound to or becomes bound to asurface and a second of the NSSBPs is bound to or becomes bound to adetectable label.
 2. A method for performing an assay for a bonded pairof polynucleotide sequences comprised of first and second specificnucleotide sequences in a sample suspected of containing the bondedpair, hybridized to the same target polynucleotide sequence, whichmethod comprises:a) providing in combination in a liquid medium (1) thesample, (2) first and second nucleotide sequence specific bindingproteins (NSSBP) that bind, respectively, to the first and secondspecific nucleotide sequences wherein the first NSSBP is bound orbecomes bound to a surface and the second NSSBP is bound to or becomesbound to a detectable label, and (3) the surface if said first NSSBP isnot bound to a surface; b) separating the medium from the surface; c)combining the surface with a detectable label that binds to the secondNSSBP, when the second NSSBP is not already bound to a label, thebinding thereof indicating the presence of said bonded pair ofpolynucleotide sequences hybridized to the same target polynucleotidesequence; and d) detecting the label bound to the surface.
 3. The methodof claim 2 wherein the label is a nucleic acid sequence.
 4. The methodof claim 2 wherein the label is selected from a group consisting of anenzyme, catalyst, fluorophore, chemiluminescer, light absorbent dye andmetal cluster.